So, Chroma's 1 breathes an element, whichever one you have equipped from your energy color. 2 gives a AOE effect from your element, and 3 is a damage and armor buff.
So, from your description, it seems to be working normally, unless you had infinite duration, or no energy drain.
https://warframe.fandom.com/wiki/Chroma#Abilities

DE is trying to unify the UI between console and PC, so that when the new UI comes out, or they make another update for it, it is easier to ship it to both platforms. Easier to bugfix, and easier to work on, if you only have to make one control scheme work, rather than bugfixing console and PC UI separately.
It isn't going away.

They addressed this on the devstream. Due to people already researching it, the cost will stay the same, but they are looking into buffing the drops of mutagen samples, or making them drop 2-3 per time.

Mag p is the only vaulted frame you can still farm for with relics. The other unvaulted frames were never in relics, so they can't be farmed out of them. When they vaulted mag p, they made a new relic, which drops in ODS, that had the rest of the parts on the vaulted relics. so that is most likely why you got mag p relics left over, since they made a new relic, and you wouldn't have any corresponding keys that would translate into relics for that.

From what i understand, any non maxed mods will be at the same rank. The only thing that will happen is that and extra fusion energy (partial bar underneath the mod) will be converted to endo. This shouldn't erase partially fused mods, just bring them down to the baseline where the new system can properly fuse them to the next levels.
Keep in mind that this is just how I interpret what this thread says.